Chewbbaca

We've developed [Chewie-NS](https://chewbbaca.online/), a Nomenclature Server that is based on the [TypOn](https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-43) ontology and integrates with chewBBACA to provide access to gene-by-gene typing schemas and to allow a common and global allelic nomenclature to be maintained.

To allow all users to interact with the Chewie-NS, we've implemented the following set of modules:

- `LoadSchema`: enables upload of new schemas to the Chewie-NS.
- `DownloadSchema`: enables download of any schema from the Chewie-NS.
- `SyncSchema`: compares local schemas, previously downloaded from the Chewie-NS, with the remote versions in the Chewie-NS to download and add new alleles to local schemas, submit new alleles to update remote schemas and ensure that a common allele identifier nomenclature is maintained.
- `NSStats`: retrieves basic information about species and schemas in the Chewie-NS.

The [documentation](https://chewie-ns.readthedocs.io/en/latest/) includes information about the integration with chewBBACA and how to run the new [LoadSchema](https://chewie-ns.readthedocs.io/en/latest/user/upload_api.html), [DownloadSchema](https://chewie-ns.readthedocs.io/en/latest/user/download_api.html), [SyncSchema](https://chewie-ns.readthedocs.io/en/latest/user/synchronize_api.html) and [NSStats](https://chewie-ns.readthedocs.io/en/latest/user/nsstats_api.html) processes.
The Chewie-NS [source code](https://github.com/B-UMMI/Nomenclature_Server_docker_compose) is freely available and deployment of local instances can be easily achieved through Docker Compose.

This version also includes other changes:

- The `AlleleCall` process will detect if a schema was created with previous chewBBACA versions and ask users if they wish to convert the schema to the latest version. The conversion process **will not alter** your schema files, it will simply add configuration files and copy the Prodigal training file to the schema's directory. You can force schema conversion with the `--fc` argument.
- It is now required that users provide a valid Prodigal training file to the `CreateSchema` and `PrepExternalSchema` processes. The training file will be included in the schema and can be automatically detected by the `AlleleCall` process.
- Schemas created with the `CreateSchema` process or adapted with the `PrepExternalSchema` retain information about parameters values (BLAST Score Ratio, Prodigal training file, genetic code, minimum sequence length and sequence size variation threshold) and users are advised to keep performing allele call with those parameters values to ensure consistent results and provide the possibility of schema upload to the Chewie-NS. The AlleleCall process detects if a user provides parameters values that differ from the original values and requests confirmation before proceeding (you may force execution with the `--fc` argument).
- The AlleleCall process creates a SQLite database in the schema's directory that is used to store the allelic profiles determined with that schema.
- Further optimizations in the `PrepExternalSchema` process.

- New `PrepExternalSchema` implementation: algorithmic optimizations to improve speed and maintain memory efficiency. New output files with summary information about schema adaptation and excluded sequences and options to control the Blast Score Ratio, minimum sequence length and genetic code values passed to the process.

chewBBACA released as a galaxy module!

Many Thanks to Stefano Morabito and Arnold Knijn (https://github.com/aknijn) for EURL VTEC in ISS, Rome!
https://toolshed.g2.bx.psu.edu/repository?repository_id=88fd7663075eeae9&changeset_revision=093352878303

- New alleles also have a timestamp added to the allele name.

- Corrected bug from 2.0.15 when no Prodigal training file was provided.

- Added Prodigal training files to the package. Available at `CHEWBBACA/prodigal_training_files`.

- When using the function `PrepExternalSchema`, older behavior would remove any locus with a single translation error while the latest change (2.0.12) would not change the original source fasta, which would make the schema unusable. It is now enforced that the alleles that do not translate are removed from the fasta, be sure to backup your data before using this function.